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1 : olson 1.1 <pre>
2 :     Higher Level Constructs
3 :    
4 :     The Higher Level Constructs table provides a way to define entities
5 :     that can be formed from gene products.
6 :    
7 :     For exqample, if a multi-meric enzyme comprises subunits alpha and
8 :     beta, we would put two roles in its subsystem, one for each subunit.
9 :     Those roles might have one, none, or several genes assigned to them
10 :     according to what is present in the organism.
11 :    
12 :     The Higher Level Constructs tool provides a means to express these
13 :     constructs. The tool is a simple table with two columns, "Construct Name"
14 :     and "Requires."
15 :    
16 :     In "Construct name" enter the name of the Construct your are defining, e.g., GOGAT_NADPH.
17 :     In the "Requires" column, enter a comma separated list of all the things that are
18 :     required in order for the construct to be present. In other words, it is a list that
19 :     is AND-ed together.
20 :    
21 :     Each entry in the requirements list can be one of two things. It can either be the
22 :     abbreviation for a functional role or it can be the name of another construct. For
23 :     convenience, you do not need to enter the abbreviation, but can enter the row number
24 :     and, when you hit the "Update" button, the row number will be converted to the
25 :     abbreviation for you.
26 :    
27 :     A Construct name can be listed multiple times. This corresponds to OR's. For
28 :     example:
29 :    
30 :     Constsruct Name Requires
31 :     GOGAT_NADPH GOGDP1, GOGDP2
32 :     GOGAT GOGAT_NADPH
33 :     GOGAT GOGATF
34 :     GOGAT GOGATD
35 :    
36 :     This table says that GOGAT_NADPH is present when GOGDP1 AND GOGDP2 are both
37 :     present. These are abbreviations of functional roles in the Ammonia Assimilation
38 :     subsystem. Also, GOGAT is present when either GOGAT_NADPH or GOGATF or GOGATD
39 :     are present. GOGAT_NADPH is the Construct defined in the first line. The other
40 :     two are abbreviations of subsystem roles.
41 :    
42 : golsen 1.2 </pre>

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